It is the clerk's issue or meet administration (NCAA) issue for allowing the kid to line up in the 5k to begin with. If that had properly occurred, then the Harvard coach would not have had to act to request enforcement of a rule.
The VA TECH coaches have a responsibility to know the rules and to follow them. The consequence falls on the athlete because of the VA TECH coaches not knowing the rules of their profession. While the athlete at VA TECH deserves sympathy, it is not the fault of the Harvard coaches.
Reinstating him may create a bad precedent moving forward. I hope the VA TECH coaches learn a lesson from this and extend it to all aspects of their job. When they fail, student-athletes often suffer. I hope the NCAA puts into place a system for monitoring DNFs at the NCAA preliminary round.
"don't punish the student-athelte for my mistake" doesn't cut it. there simply has to be consequence for there to be order in a society.